The Search Bar is the central querying interface. It supports natural language queries of neurons, synaptic partners, etc. By combining various attributes of query targets, you can create some very powerful queries.

Your queries should start with a verb; the verbs supported right now are:
• show: clear workspace and then show the queried neurons,
• add: add to the workspace the neurons queried,
• remove: remove from the workspace the queried neuron,
• keep: keep in the workspace only the neurons that meet the criterion of the query,
• hide: hide the neurons that meet the criterion of the query (this does not remove them from workspace, but reduce their visibility),
• pin: pin the neurons that meet the criterion of the query. Pinned neurons are automatically highlighted, and cannot be removed by the "trash can" button on top of the NeuroNLP window.
• unpin: unpin the neurons that meet the criterion of the query,
• color: color the neurons that meet the criterion of the query with a user defined color (can be hex color code, e.g., FF0000 for red), or these predefined colors.

Additionally, the following single word commands are supported:
• clear: clear up the workspace, removing all neurons and synapses,
• undo: undo your last query.

Next, we explain the rules for defining the criterion of the query, using the verb "show" as an example.
• show $string$ neurons: Shows neurons with a name that contains the string. Example:
  • show $E0585$ neurons, or simply show $E0585$, will query any neuron whose name contain the string *E0585*.
• show /rstring/r neurons: Show neurons whose name matches the regular expressing string (This requires some knowledge of how the neurons are named in each dataset). Example:
  • show /r(.*)TH-F-[1-2](.*)2/r neurons, or simply show /r(.*)TH-F-[1-2](.*)2/r will show dopaminergic neurons (TH gene) with the FlyCircuit ID number starting with 1 or 2 and end with 2
• show neurons in|that innervate|that arborize in neuropil/subregion: Shows neurons that has output or input in a neuropil or a subregion of a neuropil. Examples:
  • show neurons in ellipsoid body, or using abbreviations show neurons in EB,
  • show neurons that innervate right al and right mb. Note that this is different from show neurons that innervate right al or right mb.
• show local neurons in neuropil: Shows the neurons that has only inputs and outputs within the neuropil (note that due to lack of data in some datasets, some neurons are only traced in one neuropil and thus are classified local neuron by default). Examples:
  • show local neurons in ellipsoid body
• show neurons with|that have inputs|outputs in neuropil/subregion: More specific then the previous query on the inputs or outputs. Examples:
  • show neurons with inputs in OPTU
  • show neurons with inputs in right antennal lobe and outputs in right lateral horn, or equivalently show neurons projecting from right antennal lobe to right lateral horn,
  • show neurons that connect right AL and right MB. Includes both the neurons that has inputs in AL and outputs in MB, and those has inputs in MB and outputs in AL.
• show neurons presynaptic|postsynaptic to: Shows the neurons that are presynaptic or postsynaptic to the neurons defined after the word to. Exmples:
  • show neurons presynaptic to $TH-F-700014$ in right medulla
  • show $Cha$ presynaptic to $TH-F-700014$
• show presynaptic|postsynaptic neurons: Shows the neurons that are presynaptic or postsynaptic to the neurons already in workspace. Examples:
  • show presynaptic neurons,
  • show postsynaptic neurons with at least 10 synapses.
• show neurotransmitter neurons: Shows the neurons that express a specified neurotramsitter. Examples:
  • show GABAergic neurons in EB
  • show cholinergic presynaptic neurons
  • show glutamatergic local neurons in AL

Other short-hands:
• show /:referenceId:[VGlut-F-000001, Cha-F-100201]: Shows the neurons whose referenceId in the original dataset is in the list. It can be used similar to "$string$" syntax and regular expression syntax "/rstring/r" described above, and they can be combined with other types of criteria. Examples:
  • show /:referenceId:[VGlut-F-000001, Cha-F-100201]

Coloring: if no criteria are specified, the color will be applied to the neurons added in the most recent query. For example, if you query: show A neurons, then add B neurons, color red will color B neurons red. color A neurons 0000FF will then color A neurons blue.

To use your mouse to navigate in the 3D visualization:

Try out the "Pin/Select/Highlight" Demo (GUI Usage #3 in the Demos).

Translation

Right-click and then drag the cursor to translate the entire 3D scene.

On mobile and tablets, the scene can be translated by dragging with three fingers.

Rotation

Left-click and then drag the cursor to rotate the entire 3D scene.

On mobile and tablets, touch and drag with one finger to rotate the scene.

Zoom

Scroll up or down to zoom in or out the entire 3D scene.

On mobile and tablets, pinch out or in to zoom out or in respectively.

Highlight a Neuron/Synapse

Hover over a neuron/synapse will highlight that neuron, with all other objects dimmed (except for those pinned). Brightness of highlighted objects and dimmed objects can be respectively adjusted in the Visualization Settings (see also Visualization Settings below).

Select a Neuron/Synapse

Hover over a neuron/synapse and Left-Click to retrieve the detail information in the Info Panel.

On mobile and tablets, touch on the neuron with a single finger to select it.

Pin a Neuron/Synapse

Hover over a neuron/synapse and Double-Click to pin it in the scene. Pinned neurons will always be highlighted. Brightness of pinned objects and unpinned objects can be respectively adjusted in the Visualization Settings (see also Visualization Settings below).

After pinning neurons of interest, you can use the remove unpinned neurons icon (  ) to restrict the workspace to neurons you are interested in.

On mobile and tablets, select a neuron and then touch and hold on it for at least 750ms to pin it.

Try out the "Visualization Panel Buttons" Demo (GUI Usage #4 in the Demos).

Here we list the function of each button:

• : Open visualization settings.
• : Open this menu.
• : Turn on/off stats performance monitor.
• : Take a screenshot of the current 3D visualization. The quality of the screenshot depends on the resolution of the display and the browser window size.
• : Reset view to original setting.
• : Zoom in onto the visualized (not hidden) neurons.
• : Show all neurons, synapses and neuropils.
• : Hide all unpinned neurons/synapses.
• : Remove all unpinned neurons/synapses.

Try out the "Graph View / Connectivity Buttons" Demo (GUI Usage #5 in the Demos).

Three additional buttons in the Visualization Panel provide information about the graph of the visualized neural circuit:

• : Open the Graph View to generate a neuronal level graph of the neurons in the current workspace. The graph is visualized in 2D. Nodes representing each neuron has the same color as in the 3D visualization. Nodes can be reordered by dragging them. Hovering over a node will highlight the corresponding neuron in the 3D visualization. Clicking on the node hide/unhide morphology of the corresponding neuron. You can adjust the synapse threshold to remove connections that has less number of synapses than the value.
• : Open the Graph View to generate a cell type level graph of the neurons in the current workspace. Connections from all neurons of one cell type to all neurons of another cell type will be aggregated. Nodes can be reordered by dragging them. Hovering over a node will highlight the neurons of the corresponding cell type in the 3D visualization. Clicking on a node hide/unhide morphology of the neurons of the corresponding cell type.
• : Download the graph in CSV format, that includes the pre-synaptic neuron name, post-synaptic neuron name and the number of synapses on each row.

You can customize the visual effects in the Visualization Panel by using the Visualization Settings menu. Here is a break down of the options.

Backgound

• Color: change the color of the background of the Visualization Panel.

Neuron Rendering

• Rendering Mode: change the way neuron morphology is rendered.
• Default Neurite Radius: If the neuron skeleton does not contain radius information, this is the default value that will be used.
• Neurite Radius Range: The range of acceptable radius. Any radius outside of this range will be clipped to the nearest acceptable range.
• Default Soma Radius: If the soma of the neuron skeleton does not contain radius information, this is the default value that will be used.
• Soma Radius Range: The range of acceptable radius of soma. Any radius outside of this range will be clipped to the nearest acceptable range.
• Default Opacity: The opacity of visualized neurons/synapses when none of them are highlighted or pinned.
• Higlighted Neuron Opacity: The opacity of the neuron/synapse being highlighted.
• Low Opacity in Highlight Mode: When a neuron/synapse is highlighted, the opacity of the rest of the neurons/synapses.
• Pinned Neuron Opacity: The opacity of pinned neurons/synapses.
• Low Opacity in Pinned Mode: When some neurons/synapses are pinned, the opacity of the unpinned neurons/synapses.
• Ambient Light: Brightness of ambient light onto neurons/synapses.
• Directional Light: Brightness of directional light onto neurons/synapses.

Neuropil Rendering

• Color: Color of the Neuropil meshes.
• Opacity: Opacity of the Neuropil meshes.
• Wireframe Opacity: Opacity of the wireframe on the Neuropil meshes.
• Screen-space ambient occlusion pass (SSAO): Whether to enable SSAO effect.
• Ambient Light: Brightness of ambient light onto neuropils.
• Directional Light: Brightness of directional light onto neuropils.

Synapse Rendering

• Synapse Size: Synapses are renders as a sphere with a radius specific by the value of Synapse Size.
• Synapse Size Range: Range of valid synapse size if they are specified in the data. If the synapse size is outside of this range, it will be clipped.
• Synapse Opacity: The opacity of the synapses when no neuron/synapse is highlighted or pinned.

PostProcessing Settings

• Fast approXimate Anti-Aliasing (FXAA): Better anti-aliasing.
• Bloom Pass: Create a glowing effect.